Simply putting the files into the Calibre folder structurewill not make Calibre see them. I suspect that you will have to add them all back in via the "Add Books" facility.
Just for interest how did you delete the old TXT format files - vai Calibre or directly using Operating System level facilities. You should always do this sort of thing via calibre if you want to keep Calibre in step with the underlying file system.
I tend to not delete old file formats as disk space is cheap and I may want to come back and convert again for some reason. Calibre does not mind keeping multiple formats of the same book around.